PRIDB

PRIDB catalogs structural protein–RNA interface annotations extracted from Protein Data Bank (PDB) complexes to enable analysis of protein–RNA interactions and their determinants.

Key Features:

• Database contents: Structural interface information for 926 distinct protein–RNA complexes from the PDB (as of October 10, 2010).
• Interface mapping in primary sequence: Identification and mapping of interfacial amino acids and ribonucleotides onto the primary sequences of interacting protein and RNA chains.
• Motif annotation: Identification of ProSite motifs in protein chains and FR3D motifs in RNA chains.
• External database links: Direct links to motif annotation resources and corresponding PDB structure files for cross-referencing.
• 3D visualization: Integrated JMol applet for visualization of contacting atoms and residues within three-dimensional complex structures.
• Automated dataset generation: Automated generation of user-defined protein–RNA interface datasets with downloads in machine-readable formats and provision of several non-redundant benchmark datasets for method development and testing.

Scientific Applications:

• Interface characterization: Detailed examination of individual protein–RNA interfaces and their interaction determinants.
• Motif–function analysis: Correlation of ProSite and FR3D motif occurrences with interface locations and potential functional roles.
• Structural inspection: Analysis of spatial interface geometry and contacting atoms/residues using PDB structures and JMol visualization.
• Benchmarking and method development: Development, evaluation, and comparative testing of predictive models using non-redundant benchmark datasets.
• Computational dataset assembly: Creation of machine-readable datasets for downstream computational analyses of protein–RNA interactions.

Methodology:

Extraction of interface annotations from PDB protein–RNA complexes; mapping of interfacial amino acids and ribonucleotides onto primary sequences; identification of ProSite motifs in proteins and FR3D motifs in RNAs; automated generation of non-redundant benchmark datasets and machine-readable dataset exports.